Preacher Safwat Hegazy was arrested close to Egypt's border with Libya in the west of the country, a military source told AFP.
Hegazy had been on the run after a warrant was issued for his arrest following last month's ouster of president Mohamed Morsi, a Brotherhood member.
Mourad Ali, a spokesman for the Brotherhood's Freedom and Justice party, was "arrested at Cairo airport as he tried to leave for Italy," a security source said.